Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F5 I177 R1	141	27.5	996908	97.7%	973979	124.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	625,777	A→G	D143G (GAC→GGC)	cstA →	pyruvate/proton symporter CstA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	625,777	0	A	G	100.0%	79.4 / NA	24	D143G (GAC→GGC)	cstA	pyruvate/proton symporter CstA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (11/13); total (11/13)

AGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCT  >  NZ_CP009273/625643‑625906

aGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGt                                                                                                                               >  2:285484/1‑139 (MQ=255)

     gTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGtcgctc                                                                                                                          >  2:113787/1‑139 (MQ=255)

          cTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTgg                                                                                                                     >  1:441128/1‑139 (MQ=255)

                                 gcAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATg                                                                                              >  1:147746/1‑139 (MQ=255)

                                        ggCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCaa                                                                                       <  2:259966/139‑1 (MQ=255)

                                             ccTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAAccgc                                                                                   <  2:187256/138‑1 (MQ=255)

                                                 ccGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCgggg                                                                              <  1:107134/139‑1 (MQ=255)

                                                       atgatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTg                                                                        <  2:279299/139‑1 (MQ=255)

                                                         gatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGt                                                                                                                               <  1:48836/82‑1 (MQ=255)

                                                         gatCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGt                                                                                                                               >  2:48836/1‑82 (MQ=255)

                                                               gctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCtggtg                                                                >  1:190132/1‑139 (MQ=255)

                                                               gctgctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCtgg                                                                  <  1:301516/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:484305/137‑1 (MQ=255)

                                                                   ctCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  2:147746/137‑1 (MQ=255)

                                                                                ttCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCAt                                               >  1:214334/1‑139 (MQ=255)

                                                                                     gCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              <  1:482346/119‑1 (MQ=255)

                                                                                     gCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGc                                                              >  2:482346/1‑119 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCAt                                         <  1:449206/135‑1 (MQ=255)

                                                                                          tgcggtgcAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCAt                                         >  2:449206/1‑135 (MQ=255)

                                                                                                         cATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGc                       >  1:483023/1‑138 (MQ=255)

                                                                                                                       tttCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGa         <  1:113787/138‑1 (MQ=255)

                                                                                                                             cgcgCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGcc    <  2:483023/137‑1 (MQ=255)

                                                                                                                             cgcgCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCt  <  2:149662/139‑1 (MQ=255)

                                                                                                                             cgcgCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCt  >  1:237412/1‑139 (MQ=255)

AGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCT  >  NZ_CP009273/625643‑625906

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACT  >  NZ_CP009273/625638‑625910

agaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagTGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGC                                                                                                                            <  SRR3722131.189540/90‑1 (MQ=60)

GCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGC                                                                                                                            <  SRR3722131.219001/151‑1 (MQ=60)

    gagatctagtacggtctcgtgggctcggagatgtgtataagagacagCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGG                                                                                                                        <  SRR3722131.49344/104‑1 (MQ=60)

    GAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGG                                                                                                                        >  SRR3722131.445868/1‑151 (MQ=60)

                           GTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGGGAGCTGGTCAAAGAAGAGATGG                                                                                                 >  SRR3722131.149472/1‑151 (MQ=60)

                                                     GCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTG                                                                       <  SRR3722131.108303/151‑1 (MQ=60)

                                                         GGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGG                                                                   >  SRR3722131.192315/1‑151 (MQ=60)

                                                                   GGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTT                                                           <  SRR3722131.304957/149‑1 (MQ=60)

                                                                      aagagacaGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                       <  SRR3722131.487520/142‑1 (MQ=60)

                                                                       GCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGA                                                       <  SRR3722131.489494/149‑1 (MQ=60)

                                                                          CGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATG                                                  >  SRR3722131.216882/1‑151 (MQ=60)

                                                                                          GCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAG                                  <  SRR3722131.454043/151‑1 (MQ=60)

                                                                                                   GTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGGGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCG                          >  SRR3722131.488203/1‑150 (MQ=60)

                                                                                                                    GCTATTTCTTTCTACGCGCCTTGGCGGTCGCTCGCTTGGTGAGCTGGTCAAAGAAGAGATGGGGCCATCCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCC        <  SRR3722131.208154/151‑1 (MQ=60)

                                                                                                                       GTTTGTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTG     >  SRR3722131.240224/1‑151 (MQ=60)

                                                                                                                           GTTTCTACGCGCCGTGGCGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACT  <  SRR3722131.115049/150‑1 (MQ=60)

GCCGGAGCAGGTCCGCTGGTGGGGCCGGTACTGGCGGCGCAAATGGGCTACCTGCCGGGGATGATCTGGCTGCTCGCTGGGGTGGTTCTCGCCGGTGCGGTGCAGGATTTCATGGTGCTGTTTGTTTCTACGCGCCGTGACGGTCGCTCGCTGGGTGAGCTGGTCAAAGAAGAGATGGGGCCAACCGCCGGGGTGATTGCGCTGGTGGCCTGCTTTATGATCATGGTCATTATCCTTGCAGTGCTGGCGATGATCGTGGTGAAAGCCCTGACT  >  NZ_CP009273/625638‑625910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`